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Bioinformatics Advance Access originally published online on April 25, 2007
Bioinformatics 2007 23(13):1694-1696; doi:10.1093/bioinformatics/btm148
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TFmodeller: comparative modelling of protein–DNA complexes

Bruno Contreras-Moreira *, Pierre-Alain Branger and Julio Collado-Vides

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av.Universidad, s/n, 62210 Cuernavaca, Morelos, México

*To whom correspondence should be addressed.


  Abstract

Summary: Interactions between proteins and DNA molecules lie at the core of the fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally described at atomic scale, but the molecular details of many others remain to be discovered. TFmodeller exploits the current knowledge about protein–DNA interfaces contained in the Protein Data Bank and uses it to model similar interfaces related by homology. Results are emailed to the user and include an evolutionary contact matrix, a schematic representation of the putative binding interface and atomic coordinates of the modelled complex. The library of complexes used by TFmodeller is updated on a weekly basis and is available for download.

Availability: TFmodeller and its web service interface are free for academic users at http://www.ccg.unam.mx/tfmodeller

Contact: contrera{at}ccg.unam.mx

Associate Editor: Anna Tramontano

Received on March 15, 2007; revised on April 11, 2007; accepted on April 12, 2007

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Home page
 Nucleic Acids ResHome page
B. Contreras-Moreira
3D-footprint: a database for the structural analysis of protein-DNA complexes
Nucleic Acids Res., September 18, 2009; (2009) gkp781v1.
[Abstract] [Full Text] [PDF]


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